scholarly journals Phylogenetic Group of Escherichia coli Isolates from Broilers in Brazilian Poultry Slaughterhouse

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Fernanda M. Coura ◽  
Soraia A. Diniz ◽  
Marcos X. Silva ◽  
Thiago L. M. Arcebismo ◽  
Silvia Minharro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Respiratory Tract ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
E Coli

The aim of the study was to determine the phylogenetic groups of E. coli strains isolated from seemingly healthy broiler and broiler condemned suspected of colibacillosis in a Brazilian slaughterhouse. Samples from respiratory tract and edible giblets (liver and heart) of broilers with and without macroscopic lesions of colibacillosis were collected at slaughter. There were 84 strains isolated from broilers condemned of which 11 were obtained from swabs of the heart, 7 from the liver, and 66 from the respiratory tract. Of the 53 E. coli strains isolated from broilers not condemned, 5 were isolated from the heart, 4 from the liver, and 44 from the respiratory tract. E coli strains were tested via PCR for phylogenetic groups A, B1, B2, C, D, E, and F. Phylogroups A and B1 were the most common phylogroups of E. coli obtained from healthy and sick-appearing broiler carcasses. The results of the study showed that phylogroups B2 and E were associated with the heart samples and phylogroup A was associated with respiratory tract samples, phylogroup B1 with not condemned carcass, and phylogroup D with liver samples.

scholarly journals Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1828 ◽  
Author(s):  
Paul Katongole ◽  
Daniel Bulwadda Kisawuzi ◽  
Henry Kyobe Bbosa ◽  
David Patrick Kateete ◽  
Christine Florence Najjuka
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Susceptibility ◽  
Phylogenetic Group ◽  
Diffusion Method ◽  
Clinical Microbiology Laboratory ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Pcr Method ◽  
Tract Infections ◽  
Susceptibility Patterns

Introduction: Uropathogenic Escherichia coli (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community-acquired and 30-50% of all hospital-acquired UTIs. E. coli strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified E. coli strains into eight phylogenetic groups using the quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of UPEC strains in Uganda using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. Methods: In this cross-sectional study, 140 stored uropathogenic E. coli isolates from the Clinical Microbiology Laboratory, Department of Medical Microbiology, College of Health Sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Phenotypic detection of extended-spectrum beta-lactamase, AmpC and carbapenemases was done according to CLSI guidelines and Laboratory SOPs. Results: Phylogenetic group B2 (40%) was the most predominant, followed by A (6.23%), clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was trimethoprim-sulphamethoxazole (90.71%) and the least was imipenem (1.43%). In total, 73.57% of isolates were multi-drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). Conclusions: Our findings showed the high prevalence of MDR E. coli isolates, with the dominance of phylogenetic group B2. About 9% of E. coli isolates belonged to the newly described phylogroups C, E, F, and clade I and II.

scholarly journals Detection of virulence genes, phylogenetic group and antibiotic resistance of uropathogenic Escherichia coli in Mongolia

2017 ◽  
Vol 11 (01) ◽  
pp. 51-57 ◽  
Author(s):  
Yandag Munkhdelger ◽  
Nyamaa Gunregjav ◽  
Altantsetseg Dorjpurev ◽  
Nishi Juniichiro ◽  
Jav Sarantuya
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Virulence Genes ◽  
Wide Spectrum ◽  
Iron Acquisition ◽  
Uropathogenic Escherichia Coli ◽  
Phylogenetic Group ◽  
Diffusion Method ◽  
Phylogenetic Groups ◽  
E Coli

Introduction: The severity of urinary tract infection (UTI) produced by uropathogenic Escherichia coli (UPEC) is due to the expression of a wide spectrum of virulence genes. E. coli strains were divided into four phylogenetic groups (A, B1, B2 and D) based on their virulence genes. The present study aimed to assess the relationship between virulence genes, phylogenetic groups, and antibiotic resistance of UPEC. Methodology: A total of 148 E. coli were tested for antimicrobial resistance against 10 drugs using the disk diffusion method. The isolates were screened by polymerase chain reaction (PCR) for detection of virulence genes and categorized into the four major phylogenetic groups. Results: Phylogenetic group B2 was predominant (33.8%), followed by D (28.4%), A (19.6), and B1 (18.2%). A higher prevalence of fimH (89.9%), fyuA (70.3%), traT (66.2%), iutA (62.2%), kpsMTII (58.8%), and aer (56.1%) genes were found in UPEC, indicating a putative role of adhesins, iron acquisition systems, and protectins that are main cause of UTIs. The most common antibiotic resistance was to cephalotin (85.1%), ampicillin (78.4%) and the least to nitrofurantoin (5.4%) and imipenem (2%). In total, 93.9% of isolates were multidrug resistant (MDR). Conclusions: This study showed that group B2 and D were the predominant phylogenetic groups and virulence-associated genes were mostly distributed in these groups. The virulence genes encoding components of adhesins, iron acquisition systems, and protectins were highly prevalent among antibiotic-resistant UPEC. Although the majority of strains are MDR, nitrofurantoin is the drug of choice for treatment of UTI patients in Ulaanbaatar.

scholarly journals Characterization of commensal Escherichia coli isolates from slaughtered sheep in Mexico

2021 ◽  
Vol 15 (11) ◽  
pp. 1755-1760
Author(s):  
Jorge Acosta-Dibarrat ◽  
Edgar Enriquez-Gómez ◽  
Martín Talavera-Rojas ◽  
Edgardo Soriano-Vargas ◽  
Armando Navarro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
E Coli ◽  
New Information ◽  
Antimicrobial Resistance Genes ◽  
Uremic Syndrome

Introduction: Commensal Escherichia coli is defined as bacteria without known virulence factors that could be playing a specific role in some diseases; however, they could be responsible to disseminate antimicrobial resistance genes to other microorganisms. This study aimed to characterize the commensal E. coli isolates obtained from slaughtered sheep in the central region of Mexico. Methodology: Isolates were classified as commensal E. coli when distinctive genes related to diarrheagenic pathotypes (stx1, stx2, eae, bfp, LT, stp, ipaH, and aggR) were discarded by PCR. Identification of serotype, phylogenetic group, and antimicrobial resistance was also performed. Results: A total of 41 isolates were characterized. The phylogenetic groups found were B1 in 37 isolates (90.2%), A in 2 (4.8%), and 1 isolate (2.4%) for C and D groups. Serotypes associated with diarrhea in humans (O104:H2 and O154:NM) and hemolytic uremic syndrome (O8:NM) were detected. Thirty-three isolates (80%) were resistant to ceftazidime, 23 (56%), to tetracycline 8 (19.5%) to ampicillin, and 1 to amikacin. Six isolates (14.6%) were multidrug-resistant. Conclusions: This study provides new information about commensal E. coli in slaughtered sheep, high percentages of resistance to antibiotics, and different profiles of antimicrobial resistance were found, their dissemination constitute a risk factor towards the consuming population.

scholarly journals Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda

2021 ◽  
Vol 2 (2) ◽  
pp. 63-73
Author(s):  
Kenneth Ssekatawa ◽  
Denis K. Byarugaba ◽  
Jesca L. Nakavuma ◽  
Charles D. Kato ◽  
Francis Ejobi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Factors ◽  
Virulence Genes ◽  
Carbapenem Resistance ◽  
Phylogenetic Group ◽  
Clinical Isolates ◽  
Phylogenetic Groups ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Tract Infections

Escherichia coli has been implicated as one of the main etiological agents of diarrhea, urinary tract infections, meningitis and septicemia worldwide. The ability to cause diseases is potentiated by presence of virulence factors. The virulence factors influence the capacity of E. coli to infect and colonize different body systems. Thus, pathogenic E. coli are grouped into DEC strains that are mainly clustered in phylogenetic group B1 and A; ExPEC belonging to A, B2 and D. Coexistence of virulence and beta-lactamase encoding genes complicates treatment outcomes. Therefore, this study aimed at presenting the carbapenem resistance (CR) profiles among pathogenic E. coli. This was a retrospective cross-sectional study involving use of 421 archived E. coli clinical isolates collected in 2019 from four Uganda tertiary hospitals. The isolates were subjected to antibiotics sensitivity assays to determine phenotypic resistance. Four sets of multiplex PCR were performed to detect CR genes, DEC pathotypes virulence genes, ExPEC PAI and the E. coli phylogenetic groups. Antibiotic susceptibility revealed that all the 421 E. coli isolates used were MDR as they exhibited 100% resistance to more than one of the first-line antibiotics. The study registered phenotypic and genotypic CR prevalence of 22.8% and 33.0% respectively. The most predominant gene was blaOXA-48 with genotypic frequency of 33.0%, then blaVIM (21.0%), blaIMP (16.5%), blaKPC (14.8%) and blaNDM (14.8%). Spearman’s correlation revealed that presence of CR genes was highly associated with phenotypic resistance. Furthermore, of 421 MDR E. coli isolates, 19.7% harboured DEC virulence genes, where EPEC recorded significantly higher prevalence (10.8%) followed by S-ETEC (3.1%), STEC (2.9%), EIEC (2.0%) and L-ETEC (2.0%). Genetic analysis characterized 46.1% of the isolates as ExPEC and only PAI IV536 (33.0%) and PAI IICFT073 (13.1%) were detected. Phylogenetic group B2 was predominantly detected (41.1%), followed by A (30.2%), B1(21.6%), and D (7.1%). Furthermore, 38.6% and 23.1% of the DEC and ExPEC respectively expressed phenotypic resistance. Our results exhibited significant level of CR carriage among the MDR DEC and ExPEC clinical isolates belonging to phylogenetic groups B1 and B2 respectively. Virulence and CR genetic factors are mainly located on mobile elements. Thus, constitutes a great threat to the healthcare system as this promotes horizontal gene transfer.

scholarly journals Prevalence and characterization of Escherichia coli in the Kelantan River and its adjacent coastal waters

2020 ◽  
Vol 20 (3) ◽  
pp. 930-942
Author(s):  
Chui Wei Bong ◽  
Siong Kiat Chai ◽  
Lay Ching Chai ◽  
Ai Jun Wang ◽  
Choon Weng Lee
Keyword(s):  
Escherichia Coli ◽  
Coastal Waters ◽  
Membrane Filtration ◽  
Sea Water ◽  
Phylogenetic Group ◽  
Animal Origin ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Colony Forming Units ◽  
Phylogenetic Grouping

Abstract The presence of Escherichia coli in river and sea water may cause different levels of infections and constitutes a risk to public health. In this study, water samples were collected from 15 sites along the Kelantan River, estuaries and its adjacent coastal waters to investigate the prevalence and diversity of E. coli. A membrane filtration technique was used to enumerate E. coli and phylogenetic grouping was performed using triplex polymerase chain reaction. E. coli abundance ranged from 3.1 × 10 to 1.6 × 105 colony forming units 100 mL−1, and total suspended solids correlated significantly with E. coli abundance (r2 = 0.165, p < 0.001) and rainfall (r2 = 0.342, p < 0.001). Phylogenetic group B1 and A (59.4%) were the most prevalent, whereas groups B2 and D were least abundant. The higher abundance of phylogenetic group D at upstream sites of the Kelantan River suggested fecal contamination mainly of animal origin. Canonical-correlation analysis showed phylogenetic group B2, and phylogenetic groups A and D were greater in waters with higher inorganic nutrients (e.g. NH4, NO2 and NO3), whereas phylogenetic group B1 appeared to have better salinity tolerance between phylogenetic groups.

Characterization of multidrug-resistant Escherichia coli isolated from extraintestinal clinical infections in animals

2010 ◽  
Vol 59 (5) ◽  
pp. 592-598 ◽  
Author(s):  
Justine S. Gibson ◽  
Rowland N. Cobbold ◽  
Darren J. Trott
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Susceptibility ◽  
Animal Species ◽  
Antimicrobial Agents ◽  
Multidrug Resistant ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
Diagnostic Laboratory ◽  
E Coli

Multidrug-resistant (MDR) Escherichia coli causes extraintestinal infections in both humans and animals. This study aimed to determine whether MDR E. coli isolates cultured from extraintestinal infections in several animal species were clonal and crossed host-species boundaries, as suggested by initial characterization of a subset of canine and human isolates, or whether they represented a diverse group of host-specific strains. Isolates were obtained either from The University of Queensland Veterinary Diagnostic Laboratory or from an independent diagnostic laboratory between October 1999 and December 2007. Ninety-six MDR E. coli isolates cultured from extraintestinal clinical infections in 55 animals comprising dogs (n=45), cats (n=5), horses (n=4) and a koala (n=1) were analysed by phylogenetic grouping, antimicrobial susceptibility testing and PFGE. The isolates were cultured from the urinary tract (n=61), reproductive tract (n=11), wounds (n=11), surgical site infections (n=4) and other sites (n=9). Isolates from the same E. coli phylogenetic group with 100 % PFGE similarity and the same antimicrobial susceptibility pattern were considered to be repeat clones and excluded from further analysis. Three of the four E. coli phylogenetic groups (A, n=19; B1, n=8; and D, n=49) were represented. Analysis of PFGE similarity identified clusters of related phylogenetic group A isolates [clonal group (CG) 1] and group D isolates (CG2 and CG3), with the remainder of the isolates demonstrating diversity. The majority of CG2 isolates contained a plasmid-borne AmpC β-lactamase, imparting resistance to cefoxitin and third-generation cephalosporins, and were obtained between 2000 and 2003. CG3 isolates were sensitive to these antimicrobial agents and appeared to replace CG2 isolates as the dominant clones from 2003 to 2007. Apart from several canine and feline isolates that demonstrated clonality, PFGE profiles tended to be divergent across species. Whilst MDR E. coli isolates from extraintestinal infections in different animal species are diverse, some dominant CGs may persist over several years.

scholarly journals Detection of virulence genes in ESBL producing, quinolone resistant commensal Escherichia coli from rural Indian children

2017 ◽  
Vol 11 (05) ◽  
pp. 387-392 ◽  
Author(s):  
Salesh P Chandran ◽  
Samarpita Sarkar ◽  
Vishal Diwan ◽  
Ashish Pathak ◽  
Harshada Shah ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
School Children ◽  
Antibiotic Resistance Genes ◽  
Central India ◽  
Phylogenetic Group ◽  
Quinolone Resistance ◽  
Healthy Children ◽  
Phylogenetic Groups ◽  
Indian Children ◽  
E Coli

Introduction: Extended-spectrum β-lactamase producing commensal Escherichia coli are considered as a reservoir of antibiotic resistance genes that may be transmitted in the community. This study aimed to determine the genes coding for ESBLs, plasmid mediated quinolone resistance and virulence markers in commensal E. coli isolated from healthy school children. Methodology: ESBL producing E. coli isolates (n = 47) were obtained from 529 fecal samples of healthy school children from a rural area in central India. Multiplex PCR was used to detect the genes coding for cephalosporin and quinolone resistance, for virulence fluA, fluB, stx1, stx2, eae, bfp, lt, stII, virF, ipaH, daaE, aafII and phylogenetic groups. Results: Of the 47 ESBL producing E. coli, 41 were positive for CTXM-15, 23 for TEM-1, 8 for OXA-1and a single for SHV-12. For plasmid-mediated quinolone resistance, all the 47 isolates carried the aac(6’)-ib-cr gene, and amongst them18 were qnrS positive. Virulence gene, fluA was detected in 32,whereas eae in 14, daaE in 7 and fluB in 1. In 10 isolates, fluA and eae and in 7, fluA and daaE co-existed. Of the 47 E. coli isolates, 18 were grouped into the phylogenetic group B2, 17 in D and 12 in A. The proportion of isolates positive for fluA gene in the phylogenetic group B2 (18/18), was significantly higher than in group A (7/12) and D (6/17). Conclusion: Commensal E. coli in healthy children in rural India may serve as reservoirs of resistance towards cephalosporins and fluoroquinolones and virulence coding genes for urinary tract and diarrheal infections.

scholarly journals Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Mostafa Boroumand Boroumand ◽  
Mohsen Naghmachi ◽  
Mohammad Amin Ghatee
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Pcr Method ◽  
Tract Infections

Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. E. coli strains are divided into eight phylogenetic groups based on the new Quadroplex-PCR method, which are different in terms of patterns of resistance to antibiotics, virulence, and environmental characteristics. Objectives: This study aimed to determine the phylogenetic groups and the prevalence of drug resistance genes in E. coli strains causing UTIs. Methods: In this descriptive cross-sectional study, 129 E. coli isolates obtained from the culture of patients with UTIs were evaluated for phylogenetic groups using the new method of Clermont et al. The identification of phylogenetic groups and antibiotic resistance genes was performed using the multiplex polymerase chain reaction (PCR) method. Results: In this study, concerning the distribution of phylogenetic groups among E. coli isolates, the phylogenetic group B2 (36.4%) was the most common phylogenetic group, followed by phylogroups C (13.2%), clade I (10.1%), D (9.3%), and A (3.1%) while groups B1 and F were not observed in any of the isolates, and 20.2% had an unknown state. Also, out of 129 E. coli isolates, the total frequency of tetA, tetB, sul1, sul2, CITM, DfrA, and qnr resistance genes was 59.7%, 66.7, 69, 62, 30.2, 23.3, and 20.2%, respectively. In this study, there was a significant relationship between antibiotics (P = 0.026), cefotaxime (P = 0.003), and nalidixic acid (P = 0.044) and E. coli phylogenetic groups. No significant relationship was observed between E. coli phylogenetic groups and antibiotic resistance genes. Conclusions: The results of this study showed that strains belonging to group B2 had the highest prevalence among other phylogroups, and also, the frequency of antibiotic resistance genes and drug-resistant isolates had a higher prevalence in this phylogroup. These results show that phylogroup B2 has a more effective role in causing urinary tract infections compared to other phylogroups, and this phylogroup can be considered a genetic reservoir of antibiotic resistance.

scholarly journals PHYLOGENETIC GROUP OF ESCHERICHIA COLI IN URINE OF CHILDREN ATTENDING A MATERNAL AND CHILD CENTRE, LAGOS

2020 ◽  
Vol 7 ◽  
pp. 76
Author(s):  
Anotu Mopelola Deji-Agboola ◽  
Esther Abieyuwa Utomwen ◽  
Olubunmi Adetokunbo Osinupebi
Keyword(s):  
Escherichia Coli ◽  
Bacterial Infections ◽  
Phylogenetic Group ◽  
Bacterial Isolates ◽  
Chain Reaction ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Antibiotic Susceptibility Test ◽  
Polymerase Chain ◽  
Very High

Urinary tract infection (UTI) is one of the most common bacterial infections causing significant morbidity in children. This study determines the phylogenetic group of Escherichia coli  isolated from the urine of children attending Maternal and Child Centre,  Amuwo-Odofin, Lagos State. Clean voided midstream urine sample collected  from 215 children aged five years and below . The urine samples were culture on Mac Conkey and blood agar, bacterial 5counts greater than or equal to 1 x 10CFU/ml were regarded as positive for UTI. Identification of isolates and antibiotic susceptibility test was performed using standard methods. Polymerase Chain Reaction was used to classify the isolated E. coli into A, B1, B2 and D phylogenetic groups using presence or absence of ChuA, Yja A and TspE4C2. The prevalence of UTI was 51.2% with preponderance in male 62.7% aged 24 – 35months 75.0%. Staphylococcus aureus 19.1% followed by Pseudomonas aeruginosa 12.7% and Escherichia coli10.0% were common bacterial isolates. The isolates were highly resistant to Augmentin (71.8%) and Ampicillin 91.8%; the Escherichia coli were resistant to Augmentin 54.5% and Ampicillin 100%. The E. coli were classed into B1,A, and D phylogenetic groups with percentages of 54.5%27.3% and 18.2% respectively. , The prevalence of bacteria UTI among children in this study was very high, the isolates were highly resistant to the antibiotics tested, the E.coli belong to phylogenetic groups A, B1 and D and all were resistant to Ampicillin.

Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis

Microbiology ◽  
2005 ◽  
Vol 151 (6) ◽  
pp. 2097-2110 ◽  
Author(s):  
Kylie E. Rodriguez-Siek ◽  
Catherine W. Giddings ◽  
Curt Doetkott ◽  
Timothy J. Johnson ◽  
Mohamed K. Fakhr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Virulence Genes ◽  
Phylogenetic Group ◽  
Human Beings ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Similar Content ◽  
Tract Infections

Since avian pathogenic Escherichia coli (APEC) and human uropathogenic E. coli (UPEC) may encounter similar challenges when establishing infection in extraintestinal locations, they may share a similar content of virulence genes and capacity to cause disease. In the present study, 524 APEC and 200 UPEC isolates were compared by their content of virulence genes, phylogenetic group, and other traits. The two groups showed substantial overlap in terms of their serogroups, phylogenetic groups and virulence genotypes, including their possession of certain genes associated with large transmissible plasmids of APEC. Based on these results, the propensity of both groups to cause extraintestinal infections, and a well-documented ability of avian E. coli to spread to human beings, the potential for APEC to act as human UPEC or as a reservoir of virulence genes for UPEC should be considered. However, significant differences in the prevalence of the traits occurred across the two groups, suggesting that if APEC are involved in human urinary tract infections, they are not involved in all of them.

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